The secretion of bile is the result of active hepatocellular transport processes, most of which occur across the canalicular membrane of liver cells. Disturbance of the function and/or expression of these transporters leads to the intracellular accumulation of toxic bile acids, thereby promoting cholestatic liver cell injury. Genetically determined alterations of hepatobiliary transporter function are increasingly recognized as important risk factors for an individual's susceptibility to develop cholestasis. It has become evident that, besides the established pathogenic role of mutations in canalicular transporter genes in progressive and benign forms of familial intrahepatic cholestasis, genetics may also play an important role in acquired cholestatic syndromes, such as intrahepatic cholestasis of pregnancy or drug-induced cholestasis. This overview summarizes the physiologic function and regulation of human hepatobiliary transport systems and discusses the impact of their genetic variations for the pathophysiology of different cholestatic syndromes.